1. Field of the Invention
The present invention relates to the field of molecular biology and nucleic acid chemistry. More specifically, it relates to methods and reagents for detecting human immunodeficiency virus type 1 (HIV-1). The invention therefore has applications in the field of medicine generally, medical diagnostics specifically, and the field of molecular biology.
2. Description of Related Art
The invention of methods for amplifying specific sequences of nucleic acids, in particular, the polymerase chain reaction (PCR), makes possible the rapid detection of nucleic acids present in a sample in what was previously an undetectably low quantity (see U.S. Pat. Nos. 4,683,195; 4,683,202; and 4,965,188, each of which is incorporated herein by reference). The development and application of PCR are described extensively in the literature. For example, a range of PCR-related topics are discussed in PCR Technology--principles and applications for DNA amplification, 1989, (ed. H. A. Erlich) Stockton Press, New York, N.Y.; PCR Protocols: A guide to methods and applications, 1990, (ed. M. A. Innis et al.) Academic Press, San Diego, Calif.; and PCR Strategies, 1995, (ed. M. A. Innis et al.) Academic Press, San Diego, Calif.; each of which is incorporated herein by reference. Commercial vendors, such as Perkin Elmer (Norwalk, Conn.), market PCR reagents and publish PCR protocols.
The use of PCR and probe hybridization to amplify and detect HIV-1 nucleic acid is reviewed in Kwok, 1992, Ann. Med. 24:211-214; and Coutlee et al., 1991, Mol. Cel. Probes 5:241-259; both incorporated herein by reference. PCR-based HIV-1 detection assays are described in, for example, U.S. Pat. Nos. 5,008,182 and 5,176,775; Kellogg and Kwok, 1990, in PCR Protocols: A Guide to Methods and Applications, (ed. Innis et al.), Academic Press, San Diego, Calif.:337-347; Holodniy et al., 1991, J. Inf. Dis. 163:802-865; Jackson et al., 1991, AIDS 5:1463-1467; and Mulder et al, 1994, J. Clin. Microbiol. 32(2):292-300; each incorporated herein by reference.
Commercial kits for the amplification and detection of HIV-1 are commercially available from Hoffmann-La Roche (Nutley, N.J.). The Amplicor.TM. HIV-1 Test is an in vitro assay for the detection of HIV-1 proviral DNA. The AMPLICOR HIV-1 MONITORTM.TM. Test is an in vitro assay for the quantitation of HIV-1 RNA. The Amplicor HIV-1 Test product insert and the AMPLICOR HIV-1 MONITOR Test product insert are each incorporated herein by reference. Both of the Amplicor assays amplify HIV-1 nucleic acids using the primer pair SK462 (SEQ ID NO: 5) and SK431 (SEQ ID NO: 6), described in Mulder et al., 1994, J. Clin. Microbiol. 32(2):292-300, and referred to herein as the Amplicor HIV-1 primers.
HIV-1 displays considerable genomic sequence variability. Phylogenetic analysis of the nucleic acid sequences of HIV-1 gag and env genes is described in Myers et al, 1993, Human Retrovirus and AIDS 1993, Los Alamos National Laboratory, Los Alamos, N.Mex., incorporated herein by reference. Within the M group, subtypes A-J have been identified.
Conventional techniques of molecular biology and nucleic acid chemistry, which are within the skill of the art, are fully explained fully in the literature. See, for example, Sambrook et al., 1989, Molecular Cloning--A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.; Oligonucleotide Synthesis (M. J. Gait, ed., 1984); Nucleic Acid Hybridization (B. D. Hames and S. J. Higgins. eds., 1984); and a series, Methods in Enzymology (Academic Press, Inc.), all of which are incorporated herein by reference. All patents, patent applications, and publications cited herein, both supra and infra, are incorporated herein by reference.